Uppsala University, Department of Medical Sciences, Molecular Precision Medicine
Molecular Precision Medicine research group and the SNP&SEQ Technology Platform
Sweden
Pinned Repositories
checkQC
CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
clarity-ext
Extensions for Clarity
conformist
A conformal prediction framework implementing conformal risk control.
emil
Developer-friendly predictive modeling framework
fastq_demux
Demultiplex Illumina FASTQ files
hercules
irma-scripts
Stand-alone scripts deployed to Irma
Nordlund-ALL-subtyping
DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia
Nordlund-Backlin-2013
Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia
sisyphus
Pipeline scripts for processing and QC of Illumina HiSeq and MiSeq data
Uppsala University, Department of Medical Sciences, Molecular Precision Medicine's Repositories
Molmed/Nordlund-Backlin-2013
Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia
Molmed/emil
Developer-friendly predictive modeling framework
Molmed/hercules
Molmed/Nordlund-ALL-subtyping
DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia
Molmed/sisyphus
Pipeline scripts for processing and QC of Illumina HiSeq and MiSeq data
Molmed/Backlin-2017
Molmed/Berglund-Lindqvist-2013
Molmed/elk-herder
CLI for developing ELK configurations and groks
Molmed/role_hercules
Public Ansible role for deploying Hercules
Molmed/snpseq_packs
StackStorm packs to automate sequencing center operations
Molmed/RTCGA-CNV-Baseline-Correction
Baseline correction for TCGA copy number (CN) data
Molmed/SDashboard
A visualization app written in Shiny to show sequencing metrics
Molmed/check-sample-submission
Molmed/chiasma-docs
Documents for programs related to Chiasma
Molmed/ChiasmaBulkFileService
Web service for Chiasma, handling large files with genotype results
Molmed/ChiasmaDeposit
Auxilliary client for Chiasma, placing plates and tubes in right location at lab with use of a barcode scanner.
Molmed/ChiasmaTools
A set of small programs that are refered to in the SNP&SEQ quality system
Molmed/CustomerReports
A reporting service that is used by Chiasma, showing customer reports with genotyping statistics.
Molmed/delivery
A delivery script created for UGC, which wraps the necessary Supr interactions and mover
Molmed/ExportR
Project statistics export utility
Molmed/FPdatabase
Client for loading results from the FP instrument. (Visual Basic)
Molmed/MachineEncrypt
Generating encrypted passwords for windows apps (Chiasma)
Molmed/Marincevic-2017
Code accompanying the manuscript "Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles, by Marincevic et. al."
Molmed/molmed.github.io
Hosting web content
Molmed/piper
A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/piper
Molmed/ProjMan
Scripts and modules for interacting with the ProjMan database
Molmed/projmanr
A R package that can be used to access the ProjMan database
Molmed/SNPQualityAnalysisTool
Analysis of SNP results provided by Chiasma